Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.

Our understanding of the relationships between genes, brains, and behaviors has changed a lot since the first behavioral mutants were isolated in the fly bottles of the Benzer lab at Caltech (1), but Drosophila is still an excellent model system for studying the neurobiology of behavior. Recent advances provide an unprecedented level of control over fly neural circuits. Efforts are underway to add to existing GAL4-driver lines that permit exogenous expression of genetic tools in small populations of neurons. Combining these driver lines with a variety of inducible UAS lines permits the visualization of neuronal morphology, connectivity, and activity. These driver lines also make it possible to specifically ablate, inhibit, or activate subsets of neurons and assess their roles in the generation of behavioral responses. Here, I will briefly review the extensive arsenal now available to drosophilists for investigating the neuronal control of behavior.

Apoptotic DNA fragmentation, the hallmark of apoptosis, is mediated primarily by caspase-activated DFF40 (CAD) nuclease. DFF40 exists as a heterodimer with DFF45 (ICAD), which is a specific chaperone and inhibitor of DFF40 under normal conditions. To understand the mechanism through which the DFF40/DFF45 system is regulated, we analyzed the structural and biochemical properties of apoptotic DNA fragmentation mediated by DFF40/DFF45. Using limited proteolysis, we show that residues 1-281 of DFF45 form a rigid, crystallized domain, whereas the loop formed by residues 277-281 is accessible by trypsin. These results show that the C-terminal helix formed by residues 281-300 is dynamic and necessary for the chaperone activity of DFF45, but not for inhibition of DFF40.

Recent studies have revealed that endoplasmic reticulum (ER) disturbance is involved in the pathophysiology of neurodegenerative disorders, contributing to the activation of the ER stress-mediated apoptotic pathway. Therefore, we investigated here the molecular mechanisms underlying the ER-mitochondria axis, focusing on calcium as a potential mediator of cell death signals. Using NT2 cells treated with brefeldin A or tunicamycin, we observed that ER stress induces changes in the mitochondrial function, impairing mitochondrial membrane potential and distressing mitochondrial respiratory chain complex Moreover, stress stimuli at ER level evoked calcium fluxes between ER and mitochondria. Under these conditions, ER stress activated the unfolded protein response by an overexpression of GRP78, and also caspase-4 and-2, both involved upstream of caspase-9. Our findings show that ER and mitochondria interconnection plays a prominent role in the induction of neuronal cell death under particular stress circumstances.

Cyclin E1 (CCNE1), a positive regulator of the cell cycle, controls the transition of cells from G1 to S phase. In numerous human tumors, however, CCNE1 expression is frequently dysregulated, while the mechanism leading to its dysregulation remains incompletely defined. Herein, we showed that CCNE1 expression was subject to post-transcriptional regulation by a microRNA miR-16-1. This was evident at protein level of CCNE1 as well as its mRNA level. Further evident by dual luciferase reporter assay revealed that two evolutionary conserved binding sites on 3` UTR of CCNE1 were the direct functional target sites. Moreover, we showed that miR-16-1 induced G0/G1 cell cycle arrest by targeting CCNE1 and siRNA against CCNE1 partially phenocopied miR-16-1-induced cell cycle phenotype whereas substantially rescued anti-miR-16-1- induced phenotype. Together, all these results demonstrate that miR-16-1 plays a vital role in modulating cellular process in human cancers and indicate the therapeutic potential of miR-16-1 in cancer therapy.

The generation of functional recombinant antibodies from hybridomas is necessary for antibody engineering. However, this is not easily accomplished due to high levels of aberrant heavy and light chain mRNAs, which require a highly selective technology that has proven complicated and difficult to operate. Herein, we attempt to use an alkaline phosphate (AP)-fused form of single-chain variable fragment (scFv) for the simple identification of a hybridoma-derived, functional recombinant antibody. As a representative example, we cloned the scFv gene from a hybridoma-producing mouse IgG against branched-chain keto acid dehydrogenase complex-E2 (BCKD-E2) into an expression vector containing an in-frame phoA gene. Functional recombinant antibodies were easily identified by conventional enzyme-linked immunosorbent assay (ELISA) by employing scFv-AP fusion protein, which also readily serves as a valuable immuno-detective reagent.

Hypoxia-inducible factor- (HIF-) is a heterodimeric transcriptional activator that mediates gene expression in response to hypoxia. HIF- has been noted as an effective therapeutic target for ischemic diseases such as myocardiac infarction, stroke and cancer. By using a yeast two-hybrid system and a random peptide library, we found a 16-mer peptide named F29 that directly interacts with the bHLH-PAS domain of HIF-. We found that F29 facilitates the interaction of the HIF- heterodimer with its target DNA sequence, hypoxia-responsive element (HRE). The transient transfection of an F29-expressing plasmid increases the expression of both an HRE-driven luciferase gene and the endogenous HIF-1 target gene, vascular endothelial growth factor (VEGF). Taken together, we conclude that F29 increases the DNA-binding ability of HIF-, leading to increased expression of its target gene VEGF. Our results suggest that F29 can be a lead compound that directly targets HIF- and increases its activity.

L-ascorbic acid (Vitamin C) and peptide are both useful compounds for collagen biosynthesis in cosmeceuticals (cosmetic and pharmaceutical fields). The instability of these compounds, however, limit their application in these industries. In this report, we describe the development of a novel compound, Stabilized Ascorbyl Pentapeptide (SAP), which physically is much more stable than L-ascorbic acid in water. The inhibitory effects of this SAP compound on tyrosinase and melanin synthesis is comparable to that of L-ascorbic acid. Importantly, the SAP compound displays no cytotoxicity at a high concentration (5 mM). The ability of SAP to promote collagen biosynthesis is greater than that of L-ascorbic acid or the KTTKS peptide alone. Considering the in vitro stability and functional effects, our data strongly suggest that the SAP compound is a good candidate not only as a cosmetic ingredient, but also as a wound healing agent.

Transcriptional silencing of subtelomeric genes is associated with telomere length, which is correlated with age. Long and short telomeres in young and old people, respectively, coincide with gene repression and activation in each case. In addition, differential location of genes with respect to telomeres causes telomere position effect. There is very little evidence of the manner in which age-related telomere length affects the expression of specific human subtelomeric genes. We analyzed the relationship between telomere length and gene expression levels in fibroblasts derived from human donors at ages ranging from 0-70 years. We studied three groups of genes located between 100 and 150 kb, 200 and 250 kb, and >300 kb away from telomeres. We found that the chromatin modifier-encoding genes Eu-HMTase1, ZMYND11, and RASA3 were overexpressed in adults. Our results suggest that short telomere length-related overexpression of chromatin modifiers could underlie transcriptional changes contributing to cellular senescence.

Copper is essential but toxic in excess for aerobic organisms. Yeast transcription factor ACE1 functions as a sensor for copper and an inducer for the transcription of CUP1. In addition, ACE1 can activate the transcription of superoxide dismutase gene (sod1) in response to copper. In this study, we introduced the yeast ACE1 into Arabidopsis and analyzed its function in plant. Under high copper stress, the transgenic plants over-expressing ACE1 showed higher survival rate than the wild-type. We also found that over-expression of ACE1 in Arabidopsis increased the activities of SOD and POD, which were beneficial to the cell in copper buffering. Excess copper would suppress the expression of chlorophyll biosynthetic genes in Arabidopsis, RT-PCR analysis revealed that over-expression of ACE1 decrease the suppression. Together, our results indicate that ACE1 may play an important role in response to copper stress in Arabidopsis.

The tandem ubiquitin-interacting motif (UIM) domain located at the N-terminus of Receptor Associated Protein 80 (RAP80) plays a crucial role in ionizing radiation (IR)-induced DNA damage response. RAP80 translocates to sites of IR-induced DNA damage through interaction of its UIM domain with ubiquitinated H2A and Lys63-linked polyubiquitin chains. The exact mechanism, however, through which RAP80 associates with Lys63-linked polyubiquitin chains is not clear. Here, we show by in vitro GST-pull down assays that modifying the linker region between the tandem ubiquitin binding domains of RAP80 changes the binding affinity for Lys63-linked polyubiquitin chains and affects translocation to sites of DNA breaks. Based on these findings, we suggest that the length of the linker region between the tandem ubiquitin binding domains of RAP80 may be a key factor in the binding of RAP80 with Lys63-linked polyubiquitin chains as well as in the translocation of RAP80 to DNA break sites.